Abstract: A method of characterising a DNA sample obtained from a tumour, the method including the steps of: (a) obtaining a tumour copy number profile for the sample, (b) quantifying a set of copy number features of the copy number profile, and (c) determining exposure to one or more signatures of chromosomal instability based on the quantified features. A copy number feature is a metric that characterises a copy number event in a copy number profile. The set of features does not comprise the absolute copy number of segments in the copy number profile. The signatures of chromosomal instability have been obtained by quantifying the set of copy number features in a plurality of tumour samples, and identifying one or more mutational signatures likely to result in the copy number profiles of the plurality of tumour samples. Methods of characterising types of chromosomal instability present in samples, providing a prognosis, identifying a drug target, or identifying a therapy for a subject are also described.

Abstract: The present invention provides methods for predicting the treatment response of a cancer patient, using a tumour copy number profile for the patient. The method comprise analysing the copy number profile to assess whether the characteristics of at least one copy number feature are indicative of the presence of focal amplifications in the tumour genome, wherein the at least one copy number feature is selected from: copy number change-point, segment size and segment copy number. The patient is predicted as being likely to be resistant to treatment with an agent that induces the formation of micronuclei (e.g. doxorubicin) if the characteristics of the at least one copy number features are indicative of the presence of focal amplifications in the tumour genome. Also provided a related methods and systems.